This is looking great and I'm not just blowin smoke when I say that I'm keepin my eye on this...it rocks so far. As far as the merge...do you have 2 or more shadow layers? If they have different blending modes then those modes can get lost when merging. Personally, I just leave mine alone, but since each layer takes a chunk of memory with it I can see why the need for the merge.

Try this to see if it helps: click on the first shadow layer, create a new layer, link it to that first shadow layer, move the new layer under that first shadow layer, click on the shadow layer then merge down...this will remove layer styles (blending modes and opacity count as layer styles) while preserving the look. Do the same steps for other shadow layers then merge them together.